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2004 by the American Society of Ichthyologists and Herpetologists
Copeia, 2004(2), pp. 207–221
Small Fish in a Large Landscape: Diversification of Rhinichthys osculus
(Cyprinidae) in Western North America
D
AVID
D. O
AKEY
,M
ICHAEL
E. D
OUGLAS
,
AND
M
ARLIS
R. D
OUGLAS
We mapped 112 restriction sites in the mitochondrial DNA genome of the Speck-
led Dace (Rhinichthys osculus), a small cyprinid fish broadly distributed in western
North America. These data were used to derive a molecular phylogeny that was
contrasted against the hydrographic evolution of the region. Although haplotypic
variation was extensive among our 59 sampled populations and 104 individuals, their
fidelity to current drainage basins was a hallmark of the study. Two large clades,
representing the Colorado and Snake Rivers, were prominent in our results. The
Colorado River clade was divided into four cohesive and well-defined subbasins that
arose in profound isolation as an apparent response to regional aridity and tecto-
nism. The Lower and Little Colorado River subbasins are sister to one another and
(with the Upper Colorado River) form a large clade of higher-elevation populations
that seemingly reflect postglacial recolonization from refugia in the Middle Colorado
River. The latter subbasin is sister to the Los Angeles Basin and, thus, supports the
hypothesis of an ancient connection between the two. A haplotype from the North-
ern Bonneville was sister to the entire Colorado River clade. The Snake River clade
revealed a strongly supported Lahontan group that did not share haplotypes with
surrounding basins. It contained instead scattered sites from former Pluvial Lake
Lahontan, as well as from eastern California. It was, in turn, sister to the Owens
River, whereas Rhinichthys falcatus was sister to this larger clade. The hypothesis of
a southerly, ‘‘fishhook’’-configured tributary associated with a westward-draining Pli-
ocene Snake River was manifested by the relationship of this Lahontan clade to
upper Snake and northern Bonneville localities. The Klamath/Pit and Columbia
Rivers were sisters in a clade basal to all the above, which in turn supported the
hypothesis of a pre-Pliocene western passage of the Snake River. Our data also
suggested at least three separate ichthyofaunal invasions of California, as well as a
Bonneville Basin fragmented by a north-south connection between southeastern Ida-
ho and the Colorado River. The dual western and southern movements of R. osculus
from southern Idaho argued for a northern origin, possibly associated with Tertiary
Lake Idaho.
T
HE freshwater fishes of western North
America comprise an isolated and endem-
ic fauna. As such, they are evolutionarily unique
(Minckley and Douglas, 1991). Few species
evolved among basins; most instead originated
within basins that became transient over geolog-
ical time (Miller, 1958; Minckley et al., 1986).
During these periods of reconstructive tecto-
nism, fishes and their water sources either en-
dured in situ or were instead diverted into new-
er amalgams of older systems. The only constant
for these fishes through time was their relative
seclusion. Through the Tertiary, this isolation
was exacerbated by an ever-increasing aridity
that eventually culminated by Late Cenozoic in
numerous extinctions (Smith, 1978). These
events effectively abbreviated and molded an al-
ready isolated fauna to the extent that it became
not only depauperate in overall diversity but
also concomitantly rich in distinctive morphol-
ogies (Douglas, 1993). Our biological under-
standing of this fauna has been impeded for
more than a century by the imposing topogra-
phy of the region and by the relative inaccessi-
bility of its rivers (Minckley and Douglas, 1991).
The Escalante River, a tributary of the Colorado
River in southeastern Utah, was the last river in
the continental United States to be discovered
and named (Dellenbaugh, 1873; Stegner, 1954:
142). Thus, our knowledge base for this fauna
is at best rather fragmentary, and hence inter-
relationships among populations and species
are incompletely known.
The fishes of western North America are also
ancient. The integration of modern drainage
basins began during early Miocene and was an-
tecedent to the evolution of most Western fish
genera. The latter differentiated instead during
the tortuous 20-million-year passage into Pleis-
tocene (Smith, 1981; Minckley et al., 1986).
Many of these species are now characterized by
widespread distributions and extensive morpho-
208 COPEIA, 2004, NO. 2
logical variation (Smith, 1966; Behnke, 1992;
Stearley and Smith, 1993). In the cyprinid ge-
nus Siphateles, for example, geographic variation
occurred exclusively within basins yet was large-
ly unaffected by progressive Pleistocene desic-
cation (Hubbs et al., 1974). The endemic catos-
tomids (Pantosteus and Catostomus) also seeming-
ly differentiated within basins yet were directly
impacted by orogeny rather than aridity. Other
cyprinids and salmonids (i.e., Gila, Rhinichthys,
Oncorhynchus) demonstrated even more com-
plex patterns that apparently stemmed from an
amalgam of both processes (above), as well as
from dispersal (Miller, 1946a; Hubbs et al.,
1974; Allendorf and Leary, 1988). And finally,
morphological variability and speciation in west-
ern fishes was affected not only by age and iso-
lation but also by occasional interspecific hy-
bridization (DeMarais et al., 1992; Minckley and
DeMarais, 2000).
Those Western North American freshwater
fish genera most amenable to large-scale phy-
logeographic analyses are Oncorhynchus (Behn-
ke, 1992; Stearley and Smith, 1993; McCusker et
al., 2000), Siphateles (Hubbs et al., 1974), and
Rhinichthys (Minckley et al., 1986). The latter
contains a widespread western species (Rhinich-
thys osculus, the Speckled Dace, a ‘‘mountain-
creek type’’ sensu Miller, 1958) that has attained
its current broad distribution in part by head-
water capture and stream transfer across low di-
vides (Minckley, 1973; for review of processes,
see Bishop, 1995). This species exhibits exten-
sive morphological variation and, as such, has
suffered a long and tortuous taxonomic history
(La Rivers, 1962; Miller, 1984). For example,
when first recognized as the western genus
(now subgenus) Apocope, it was thought to com-
prise some 12 species ( Jordan et al., 1930).
However, Miller (in Miller and Miller, 1948)
stated: ‘‘The forms of Rhinichthys (subgenus
Apocope) in the West exhibit so much overlap in
their characters that most of the nominal spe-
cies are now regarded as comprising a single,
wide-ranging species, R. osculus (Girard).’’ Mor-
phological variation in this species is now rec-
ognized through application of geographic tri-
nomials (sensu La Rivers, 1962; Smith et al.,
2002). The evolutionary relationships within
this species, and how these juxtapose onto the
harsh landscape of the American West, form the
backdrop of our study.
The numerous physical and biological devel-
opments described above have had a clear and
extensive impact on the evolution of freshwater
fishes in the water-poor American West. Yet test-
ing these for strength of signal has proven to be
a difficult and nontrivial task. Morphology has
often yielded little explanatory power (but see
Douglas et al., 1999), and there has instead
been a growing emphasis on molecular meth-
ods as a means to ascertain and weigh the ve-
racity of evolutionary hypotheses. Here, mito-
chondrial (mt) DNA, because of its rapid evo-
lution, neutrality, and matrilineal inheritance,
has often proven advantageous in recovering
shared histories of closely related taxa (Avise et
al., 1987). Studies employing mtDNA data often
seem to alternate between two extrema: not
enough variation (i.e., presence of minimal
polymorphism), or too much (stochastic line-
age sorting at polymorphic sites; Moritz et al.,
1987). Moreover, as a single gene tree, mtDNA
represents only a small fraction of the total his-
tory within a sexual pedigree (Schneider et al.,
1998). In this sense, molecular studies have not
always proven to be the window to deep history
that many had expected or would desire (see,
for example, Fu, 2000).
In this study, we employed restriction en-
zymes to cut mtDNA at specific sites and map-
ping techniques (as per Dowling et al., 1996) to
identify and quantify these cleavage sites within
the mtDNA genome. The resulting data are in-
dependent variables that infer mutually exclu-
sive character states and can be rendered into
binary data that correspond to presence/ab-
sence of restriction sites. As such, they are read-
ily amendable to a large variety of analytical pro-
grams (Swofford et al., 1996). Mapped mtDNA
restriction sites were used herein to derive an
intraspecific phylogeny of R. osculus that was
juxtaposed with the hydrologic evolution of
Western North America.
M
ATERIALS AND
M
ETHODS
Sampling.—From three to seven individuals were
sampled in each of 59 populations throughout
the range of R. osculus (Fig. 1; Appendix 1).
Many (i.e., 52%) were collected by regional fish
biologists, whereas the remainder (48%) were
collected by DDO and Arizona State University
personnel. At least two populations were sam-
pled per subbasin so as to more fully represent
potentially significant regions such as the Great
Basin. In addition, three other species were also
examined as outgroups: Rhinichthys atratulus
(Rouge River, MI); Rhinichthys cataractae (Wind
River, WY; South Platte River, CO; Snake River,
ID); and Rhinichthys falcatus (Columbia River,
OR). Rhinichthys atratulus was identified as a sis-
ter species to R. osculus by Coburn and Caven-
der (1992) and Woodman (1992).
209OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
Fig. 1. (A) Major drainage basins of western North America: Colorado River (AZ, UT, WY, CO); Columbia
River (WA, OR, ID); Snake River (WA, ID, UT, WY); Sacramento River (CA, OR); Klamath River (CA, OR);
Bonneville Basin (UT, NV, ID); Lahontan Basin (NV, CA, OR); Death Valley (CA, NV). (B) Collection localities
for 61 Rhinichthys osculus samples in western North America. This paper reports analyses of 59 localities: French-
man’s Lake and Last Chance Creek are both represented by Squaw Queen Creek. Locality information is in
Appendix 1.
Mitochondrial DNA extraction.—MtDNA was ex-
tracted from mt-rich tissues (i.e., eggs, heart, liv-
er, spleen, kidney) and isolated by CsCl-gradient
centrifugation (Dowling et al., 1996). Aliquots
of purified mtDNA were digested separately by
15 hexameric restriction endonucleases (i.e.,
BamHI, BclI, BglII, BstEII, EcoRI, HindIII, MluI,
NcoI, NdeI, NheII, PvuII, SacI, SacII, XbaI, XhoI).
Success depends upon obtaining complete di-
gestion of the DNA with each enzyme. Cleavage
fragments were end-labeled with all 4
a
-
32
p
dNTPs, separated by electrophoresis through
1% agarose and 4% acrylamide gels, and visu-
alized by autoradiography. Size standards
(phage lambda DNA digested with HindIII, and
phage
FX
174RF DNA digested with HaeIII)
were included on each gel, providing estimates
of fragment size. Differences in fragment pro-
files could be readily attributed to simple losses
and gains of restriction sites, and letters were
assigned to unique profiles in order of appear-
ance. Each individual was assigned an alpha-
numeric code denoting composite mtDNA hap-
lotype compiled across 15 enzymes.
A single preparation of end-labeled DNA can
be used to map recognition sites for several dif-
ferent enzymes. The generation of comprehen-
sive mtDNA restriction-site maps becomes a rel-
atively efficient process, and these were con-
structed for 104 haplotypes. Restriction sites in
a given enzyme profile were mapped relative to
cleavage sites generated in pairwise double di-
gests by other enzymes. Five endonucleases (i.e.,
BamHI, BstEII, EcoRI, HindIII, and PvuII)
formed the foundation for every restriction
map, and three to four pairwise digestions were
performed for each of the remaining 10 restric-
tion enzymes. Although it is labor-intensive to
use multiple gel mediums and to hand-con-
struct restriction maps, these dramatically re-
duce the uncertainty regarding differential mi-
gration of very small fragments caused by sec-
ondary conformational differences (Dowling et
al., 1996). When the placement of a restriction
site was ambiguous, it was removed from the
analysis. In all, 14 such sites (8.6%) were delet-
ed.
Phylogenetic analyses.—The most widely used
strategy for finding optimal trees under a par-
210 COPEIA, 2004, NO. 2
simony approach is to employ random addition
sequences in conjunction with tree bisection-re-
connection branch swapping (Nixon, 1999).
This strategy works well when numbers of taxa
are reduced, but larger datasets (i.e., those
.
40–50 taxa) have proven problematic (Golo-
boff, 1999). This is because the latter contain
numerous composite optima (or tree islands)
that, in turn, make it difficult to identify a glob-
ally optimum tree. A large number of subopti-
mal trees are instead produced, and although
these reflect identical tree lengths, they differ
among themselves with regard to minor rear-
rangements. Their accumulation often fills sys-
tem memory to capacity and overly taxes the
patience of researchers. Thus, larger datasets of-
ten require search strategies that specifically
deal with the problem of composite optima.
One (the parsimony ratchet) was demonstrated in
Nixon (1999), whereas a second (i.e., TNT [Tree
analysis using New Technology, vers. 0.2 g; P. A.
Goloboff, J. S. Farris, and K.C. Nixon; www.
zmuc.dk/public/phylogeny]) was described in
Goloboff (1999). We employed the latter to derive
minimum length trees from an initial data ma-
trix of 104 haplotypes and 154 binary characters
by selecting the following parameters: Random
Sectorial Searches (RSS)
5
15/35/3/5; Consen-
sus-Based Sectorial Searches (CSS)
5
same as
above; Tree-Drifting (DFT)
5
30/4/0/20/0;
and Tree-Fusing (TF)
5
5 (see Goloboff, 1999,
for explanation of parameters).
A series of arguments have been presented to
support (Goloboff, 1995; Allard and Carpenter,
1996; Nixon and Carpenter, 1996) or critique
(Turner and Zandee, 1995) a posteriori char-
acter weighting as an analytical strategy. The in-
tent of the process is to increase efficiency of
phylogenetic analysis by differentially weighting
characters according to cladistic reliability (the
latter defined by Farris [1969] as the fit between
character and phylogeny). This procedure re-
moves heterogeneity from data while improving
congruence among informative and usually
more conservative characters (Allard and Car-
penter, 1996). Here, successive approximation
weighting (Farris, 1969) has been most fre-
quently used (see, for example, Wills et al.,
1998; Anderson, 2000; Platnick, 2000). In this
study, we used PAUP* (vers. 4.0b8; D. L. Swof-
ford, unpubl.) to produce a strict consensus of
the 395 fused trees from TNT. A heuristic
search was then performed in PAUP*, with trees
rooted at R. atratulus and with characters
weighted by the consistency index (CI; Farris,
1969), as determined from the consensus tree.
The CI, rather than the rescaled consistency in-
dex (RCI), was used following recommenda-
tions of Archie (1996:158), who noted that the
CI was already properly scaled between (0,1)
and thus did not require rescaling. Constant (n
5
10) and uninformative (n
5
32) characters
were given weight
5
0.
Thus, the final matrix consisted of 104 indi-
viduals and 112 parsimony-informative charac-
ters. The heuristic search employed tree bisec-
tion-reconnection (TBR), saved multiple trees
(MULTREES), kept only best trees, and used
the input tree as the starting tree. The strict
consensus from this analysis then served as in-
put for a second pass through the data, with
parameters set as above and with the CI recal-
culated from the new input tree. A majority-rule
consensus tree (identical in topology to the
strict consensus) was then derived from the re-
sulting 477 most parsimonius trees.
R
ESULTS
Restriction site variation.—Our hexameric restric-
tion sites had a relatively uniform distribution
around the mtDNA molecule, with 888 corre-
sponding base-pairs representing approximately
5.3% of the estimated 16.78 kb mtDNA ge-
nome. The total number of restriction sites gen-
erated per haplotype map ranged from 137 to
144. Evidence of length variation (i.e.,
1
100bp) was evident in one individual from the
Lahontan Basin (Oakey, 2001). A majority of
the 59 populations was represented by unique
haplotypes, ranging from one (of seven individ-
uals, Amargosa River) to five (of six individuals,
Reese River), and these were generally differ-
entiated by one or two restriction sites (Oakey,
2001). Populations from adjacent localities in
close proximity often shared the same haplo-
types. Other haplotypes were broadly distribut-
ed in larger watersheds. Several localities in the
middle Colorado, Lahontan, and Bonneville Ba-
sins (Fig. 1) revealed strongly divergent haplo-
types that exhibited phylogenetic affinity with
other basins.
Phylogenetic analysis.—Results of the weighted
MP analysis revealed that R. osculus was para-
phyletic, with a single R. falcatus from the Co-
lumbia River buried within it (Fig. 2). The tree
was rooted at R. atratulus (Michigan) and was
followed immediately by haplotypes of R. catar-
actae from eastern and western Rocky Mountain
drainages. The smaller Columbia River clade
was sister to a clade composed of the Clearwater
River
1
two divergent haplotypes from South-
ern Bonneville (i.e., SEV4 and BSC2). These
were sister to the Klamath
1
Pit clade, and this
larger clade was, in turn, sister and basal to the
211OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
Fig. 2. Majority-rule consensus of 477 trees pro-
duced in PAUP* and based on 104 Rhinichthys osculus
haplotypes and 112 restriction sites. Characters were
weighted by consistency index with constant and un-
reliable characters given weight
5
0. Original tree was
consensus of 377 most parsimonious trees produced
in TNT. Location names at tips of branches are ar-
ranged in couplets with the first name representing
the upper branch and the trailing name the second
branch. Location data are provided in Appendix 1.
western Great Basin (i.e., Lahontan) and the
Colorado River physiographic regions. The lat-
ter two formed the largest and most extensive
clades in the tree. Each exhibited geographic
subbasins within which the fidelity of mtDNA
haplotyes was quite high.
The strongly supported clade of Colorado
River dace (top, Fig. 2) was partitioned into
four geographically defined subbasins, and also
contained haplotypes from the Southern Bon-
neville and Los Angeles Basins. It consists of a
Lower Basin
1
Little Colorado River (LCR) sub-
clade is sister to these, the Upper Basin sub-
clade. The Middle Colorado subbasin is sister to
the Los Angeles River and this clade was sister
to all the above. Finally, a Northern Bonneville
haplotype (i.e., BOX1) is basal to the entire Col-
orado Basin.
A second, strongly supported Lahontan Clade
(middle, Fig. 2) was composed of individuals
from the Humboldt River
1
eastern California,
and its sister, the Owens River. Basal to the La-
hontan clade was R. falcatus. Northern Bonne-
ville and Upper Snake River haplotypes were
each, in turn, sister to the Lahontan
1
R. fal-
catus clade. Overall, haplotypes clustered within
monophyletic drainage basins that were relative-
ly resolved.
D
ISCUSSION
Phylogenetic analyses and basin fidelity.—Our anal-
yses of mapped mtDNA restriction sites revealed
a nonmonophyletic R. (Apocope) osculus. The in-
clusion of R. falcatus in the osculus-clade, and
the possible presence of additional but unde-
scribed forms in the Columbia River Basin (Pe-
den and Hughes, 1981, 1988; Hughes and Pe-
den, 1989), emphasize the need for large-scale
studies of Rhinichthys in this region. For exam-
ple, R. falcatus and R. osculus coexist across
much of the former’s distribution (Peden and
Hughes, 1988), and R. falcatus was initially in-
cluded as a member of the R. osculus group
(Hubbs et al., 1974). Thus, a more thorough
assessment of genetic variability is now required
for R. falcatus before its position in this topology
can be properly interpreted. Perhaps R. falcatus
is simply a geographic form of R. osculus, as sug-
gested by Hubbs et al. (1974) and above.
A prominent feature of our data is the re-
markably high fidelity by which R. osculus clus-
ters within designated subbasins (as synopsized
in Fig. 3). Indeed, our tree is relatively consis-
tent with the idea that western fishes differen-
tiated within basins, with each of the latter now
characterized by high endemism and few spe-
cies in common (i.e., Miller’s [1958] ‘‘centers
212 COPEIA, 2004, NO. 2
Fig. 3. Relationships among drainage basins in
western North America as inferred from mtDNA re-
striction site data for Rhinichthys osculus.
of endemism’’ concept). Yet, R. osculus was rec-
ognized by Jordan and Evermann (1896) and
Jordan et al. (1930) as a distinct species largely
because of its ‘‘morphological and geographic
cohesiveness.’’ More extensive (i.e., dense tax-
on) sampling will be required to determine
whether morphologically described subspecies
are congruent with the molecular results de-
picted herein.
Most R. osculus populations exhibited exten-
sive restriction site variation. That is, nearly ev-
ery population was represented by one or more
unique haplotypes distinguished by three re-
striction sites. This Type-III phylogeographic
pattern (Avise et al., 1987), suggests that long-
term zoogeographical barriers have not limited
gene flow. A more typical phylogeographic pat-
tern would instead reveal a few widespread ge-
notypes, with others but a few steps from the
common types. This clearly does not typify R.
osculus in western North America. Possibly, this
species maintains considerable variation be-
cause it is an ecological generalist and an ex-
tinction-resistant dispersalist (as per Smith,
1981). It has endured in a fractured landscape
by using numerous but intermittent geographic
connections that existed during the Cenozoic
and by surviving in favorable habitats with great-
er frequency than other taxa (Smith, 1978).
Thus, large gaps in haplotypic diversity created
by long-range dispersal and subsequent large-
area extinctions do not characterize R. osculus.
Instead, its ubiquitous distribution and extreme-
ly large populations (i.e., ‘‘millions,’’ per Jor-
dan, 1891) would be influential in maintaining
this diversity in the American West and in re-
tarding the time necessary for phylogenetic di-
versification. We discuss these and other aspects
in greater detail below, as we dissect each of the
well-resolved clades in our tree.
The Colorado Basin clade.—This well-supported
clade includes Upper, Middle, Lower, and Little
Colorado River subbasins, plus the Los Angeles
River and a basal Northern Bonneville haplo-
type. The high fidelity of haplotypes within sub-
basins typifies an endemism largely attributable
to the prolonged development of these reaches
as isolated segments ( Jordan, 1891; Uyeno and
Miller, 1963; Hunt, 1969). In this sense, the Col-
orado River may be far older than previously
imagined (Hershler et al., 1999; Howard, 1996,
2000). During upper Paleocene to mid-Mio-
cene, the Los Angeles and Ventura Basins re-
ceived drainage from several major eastern pre-
cursors (i.e., a lower Colorado that drained the
Sonoran provinces, and an Amargosa/Colorado
that drained the Mojave provinces; Howard,
1996, 2000). In addition, Gila (Cyprinidae)
from the Lower Colorado River Basin seemingly
diverged morphologically as a result of early to
mid-Pliocene vicariant events (Douglas et al.,
1999). These data juxtapose with the hypothesis
that the modern western ichthyofauna is indeed
ancient (i.e., Oligocene-Miocene) (Minckley et
al., 1986). We suggest that R. osculus was present
within these early and interior western drain-
ages and that our data reflect these ancient con-
nections.
Los Angeles Basin.—Haplotypes from the Santa
Ana and San Gabriel Rivers in the Los Angeles
Basin formed a well-supported monophyletic as-
semblage that was sister to the Middle Colorado
River clade. Similarly, Cornelius (1969) found
that Rhinichthys osculus carringtoni (the geo-
graphic form found in the Los Angeles Basin)
was meristically and morphologically most sim-
ilar to Rhinichthys osculus yarrowi from the Mid-
dle Colorado River than it was to R. o. carringtoni
213OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
from north-coastal and northeast California. At
least two other Los Angeles Basin fishes (i.e.,
Catostomus [Pantosteus] santaanae and Gila orcut-
ti) also have hypothesized nearest relatives in
the Lower Colorado River (Smith, 1966). Catos-
tomus (Pantosteus) santaanae probably arrived in
southern California coastal drainages as the re-
sult of an early (e.g., Pliocene) and westward-
draining Colorado River (Smith, 1966).
In our analyses, the basal nature exhibited by
the Los Angeles Basin suggests an old connec-
tion with the Middle Colorado River, followed
by a long period of isolation. It also suggests
that the Colorado River and the Pacific coastal
drainages were linked by an ancient fluvial con-
nection. However, additional studies (both ge-
netic and geologic) are needed to more fully
develop such a biogeographic synthesis (see
Minckley et al., 1986).
Lower elevation Colorado River drainages.—The
Middle Colorado Basin (i.e., Pluvial White,
Moapa, and Lower Virgin Rivers) was sister to
the Los Angeles Basin, with both sub-clades bas-
al and sister to the remaining Colorado River
haplotypes. The Middle Colorado historically
drained the southwestern margin of the Colo-
rado Plateau, and it is characterized by elevated
endemism (Miller and Hubbs, 1960). Portions
of the Middle Colorado represent the lowest el-
evations in the watershed, and the high num-
bers of haplotypes found there (Oakey, 2001)
suggest that effective population sizes were pre-
viously quite large. In addition, the Middle Col-
orado may have provided refugia for the even-
tual recolonization of higher elevation sites in
the Upper Colorado River Basin and the LCR
(W. L. Minckley, pers. comm.). The close rela-
tionship between Middle and Upper Colorado
basins is supported by the shared presence of a
morphological attribute (i.e., a frenum) in both
Upper Basin R. o. yarrowi, and Middle Basin
(i.e., Pluvial White River) Rhinichthys osculus ve-
lifer (Miller, 1984). In addition, haplotypes of
Pahranagat Valley R. o. velifer were virtually iden-
tical in our analyses with those from the Moapa
River (Oakey, 2001). These results conflict with
the interpretation of Williams (1978), who re-
garded the Moapa form as meristically inter-
mediate between R. o. velifer and R. o. yarrowi.
The close genetic relationship between R. o. ve-
lifer and the ‘‘Moapa River’’ form is not surpris-
ing, particularly since both occur within drain-
ages that are subject to intermittent flooding
(Hubbs and Miller, 1948; Miller and Hubbs,
1960).
Monophyly of Lower Colorado River R. oscu-
lus is not surprising, particularly given the com-
plex basin and range faulting that occurred
within this region during much of the Tertiary
(Nations et al., 1985). This upheaval contribut-
ed in large part to the long history of isolation
this region has experienced. The Lower Colo-
rado also revealed a high number of haplotypes
(Oakey, 2001) that, in turn, suggested the for-
mer presence of large population sizes. These
haplotypes segregated into two lineages, Verde
River/San Pedro-Santa Cruz rivers versus upper
Gila River. In a study similar to ours, Lower Col-
orado River populations of a second small cyp-
rinid (Agosia chrysogaster) were also character-
ized by relatively close affinities, a poor popu-
lation structure, and a separation of Verde River
populations from those in the upper Gila River
(Tibbets and Dowling, 1996). A founder-flush
scenario, coupled with frequent dispersal may
have enabled R. osculus to move freely through-
out this subbasin and to maintain high effective
population sizes over time, thus retarding phy-
logenetic resolution.
Upper elevation Colorado River drainages.—Streams
on the Colorado Plateau may only interconnect
during storm events and then in an unpredict-
able and ephemeral manner. Given this, it was
not unusual to find that the LCR drainage was
represented by six unique haplotypes from four
widely scattered localities. The lack of structure
in this clade may again reflect the isolation of
populations and the stochastic loss of lineages
in those that are reduced in numbers (as per
Minckley et al., 1986). Minckley (1973) also sug-
gested the possibility that R. o. osculus and R. o.
yarrowi may have intergraded chaotically across
the Mogollon Rim (the southern edge of the
Colorado Plateau in north-central Arizona) as
this region gradually eroded northward. A hint
of this is reflected in the sister relationship be-
tween the LCR with the Lower Colorado, and
particularly by the basal position of Nutrioso
Creek (NUC) in the LCR drainage, which lies
adjacent to headwater populations in the Lower
Basin.
The Upper Colorado River clade is sister to
the Lower-LCR clade and is composed of the
Green, San Juan, and upper Colorado rivers, as
well as haplotypes from the Southern Bonne-
ville. Although it contains haplotypes separated
by great geographic distances, their close ge-
netic affinities and shallow clade depth suggest
relatively young populations. Freshwater fishes
from nonglaciated areas of the northern lati-
tudes (Bodaly et al., 1992; Hansen et al., 1999;
Wilson and Hebert, 1998) demonstrate on av-
erage deeper topologies and greater genetic di-
versities than those seen above. At least 20 sep-
214 COPEIA, 2004, NO. 2
arate glacial epochs were recorded during the
Pleistocene (Martinson et al., 1987; Dawson,
1992), and higher elevation populations of R.
osculus in the upper basin may in fact represent
recent recolonization from lower basin refugia
(W. L. Minckley, pers. comm.). That is, upper
elevation fishes may have been driven to lower
elevations at onset of colder glacial periods,
only to recolonize the higher elevation sites
again during warmer interglacials. Low haplo-
type diversity may result from serial bottlenecks
(Dowling et al., 1996) as Speckled Dace pro-
gressively recolonized further upstream follow-
ing glacial retreat. This hypothesis is supported
by the relatively low number of haplotypes
found in the Upper Colorado River clade and
its sister relationship with the lower-LCR Basin.
Southern Bonneville localities were buried
within the Upper Colorado River clade. In gen-
eral, Bonneville species share closest relatives
with those found in the Upper Basin (Miller,
1958). This was also suggested by the fact that
Gila cypha (a Colorado River endemic) was
more closely related to Sevier River (i.e., Bon-
neville Basin) Gila atraria than to its Colorado
River sister species, Gila elegans or Gila robusta
(Dowling and DeMarais, 1993). Montane spe-
cies are the link between the Bonneville and
Upper Colorado Basins, and these in turn sug-
gest interbasin transfers between the two, large-
ly from headwater stream captures and drainage
reversals over low divides (Hubbs and Miller,
1948; Miller, 1958; Smith, 1978). Such a scenar-
io could explain why upper Virgin River hap-
lotypes were found in the Upper but not the
Middle Colorado River clade. The Virgin River
lies along the boundary between the Great Ba-
sin and the Colorado Plateau (Minckley et al.,
1986). Its lower portion drains basin and range
topography, whereas the upper drains the Pla-
teau. The Upper Colorado River Basin formerly
drained portions of the upper Virgin, but this
flow was reversed by the continued uplift in this
region, effectively allowing these headwater
reaches to be captured by the lower-in-elevation
Virgin River.
Lahontan (or western Great Basin) clade.—Haplo-
types from northern Great Basin (i.e., Northern
Bonneville) and those basins further west are all
basal to the Lahontan clade. These basins were
once allied to the premodern Snake River
drainage, prior to its union with the Columbia
River in late Pliocene (Malde, 1991; Smith et al.,
2000). This early Snake River was a western out-
let for Lake Idaho (now southern Idaho), a sys-
tem of heterogeneous lacustrine habitats that
formed Miocene and Pliocene. The faunas dur-
ing these two periods were spatially homoge-
neous, with each a major focus of ichthyofaunal
diversity (Smith, 1975, 1987; Middleton et al.
1985). Lake Idaho has been the subject of nu-
merous studies, at least three of which have con-
siderable bearing on the present investigation.
Taylor (1966, 1985), Miller and Smith (1967),
and Smith (1975) found that Pliocene bivalves
and fishes from Lake Idaho had closest relatives
in the Sacramento-San Joaquin and Klamath ba-
sins to the west. These disjunctions resulted
from several hypothesized drainages. One such
(i.e., the ‘‘fishhook:’’ Taylor, 1966) is believed
to have run westward from southeastern Idaho,
through southeastern Oregon and western
Great Basin, then southward along the eastern
Sierra Nevada to the Death Valley system. Nu-
merous fossil bivalves and fishes (Taylor, 1966;
1985:289, fig. 18; Taylor and Smith, 1981; Miller
and Smith, 1981) documented the existence of
this drainage. However, the timing of such an
early Snake River connection is rather uncertain
in part because of vast temporal and spatial in-
tervals coupled with imprecise dating of fossils
(Smith et al., 2000). The sister-relationship of
the Columbia
1
Upper Snake to the Lahontan
and other western basins suggests that northern
R. osculus has been strongly influenced by ear-
lier basin alignments and by several connections
to the early Snake River.
The interior of the Lahontan clade consists
of fluvial localities in the Humboldt River drain-
age, as well as high-desert isolates scattered
widely in the former basin. This region was iso-
lated as the Sierra Nevada Mountains uplifted
during late Plio-Pleistocene. It is characterized
not only by high levels of endemism but also by
extensive variation within and among its wide-
spread forms (Hubbs and Miller, 1948; Hubbs
et al., 1974). The high number of mtDNA hap-
lotypes within the interior of the clade suggest-
ed the former presence of a metapopulation,
with influences extending as far west as the
closed basins of eastern California. As demon-
stration, 45 unique haplotypes were recovered
from 60 individuals (e.g., Reese River); none
was shared with the Bonneville, Columbia, or
Colorado Basins (Oakey, 2001). The interior of
the Lahontan clade was, however, poorly re-
solved and exhibited a confusing geographic
structure. This is likely attributable to a long his-
tory of intermittently connected habitats that
displayed numerous secondary contacts, cou-
pled with incomplete lineage sorting of ances-
tral variation. A similar stochastic structure was
also evident in Cyprinodon from Death Valley
(Duvernell and Turner, 1998).
The Lahontan clade consisted of a well-sup-
215OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
ported interior, plus an apical-to-basal progres-
sion that runs westward to eastern California,
and southwest to the Owens/Amargosa system.
The eastern California and Owens River locali-
ties, on the eastern front of the Sierra Nevada
Mountains, represented the southern extension
of the fishhook distribution (discussed above).
Our eastern California locations consisted of
Lake Almanor, Eagle, and Honey Lakes and
sites in the upper Feather River that lie on a
plateau between the Sierra Nevada and its east-
ern escarpment. Honey and Eagle Lake Basins
are now closed systems, and several impassable
canyons resulting from the developing escarp-
ment on the western slope of the Sierra Nevada
now protect the upper Feather River (Moyle,
1976). We speculate that these older Snake Riv-
er haplotypes have persisted by simply occupy-
ing protected, hanging tributaries and, thus,
represent, in part, the original Lahontan form
of R. osculus.
Owens River clade.—A strongly supported
(100%) Owens River clade is basal to the La-
hontan and represents two mainstream locali-
ties in addition to Amargosa River and Whit-
more Hot Springs (WHS). The latter is isolated
behind a 0.7-million-year-old caldera (Hill et al.,
1985) and may retain R. osculus haplotypes from
an earlier period. Our results corroborated Mill-
er (1946b) who suggested that Owens River R.
osculus spilled across Mono Basin and into
Owens Valley, but physical evidence for this
event was obscured by volcanic ash (Hubbs and
Miller, 1948). Again, the lack of a close relation-
ship between Owens River and the Los Angeles
Basin corroborates the earlier morphological
studies of Cornelius (1969).
The close affinity between Amargosa and
Owens Rivers is likely caused by their occasional
fusion as Lake Manley enlarged during years of
extreme precipitation (Miller, 1946b). However,
Miller (1946b, 1984) also argued that R. osculus
in the Amargosa River were closely allied to
those in the Colorado River, as the former was
briefly connected to the latter by Pluvial Las Ve-
gas Wash, a flood-tributary. Similarly, Howard
(1996, 2000) suggested that both the Amargosa
and Gila paleorivers drained the Los Angeles
Basin and were later joined by the Colorado Riv-
er after it diverted southward in Late Miocene.
However, our data fail to link the Amargosa and
Colorado Rivers. The Amargosa Basin is instead
a geological as well as biological composite with
relationships both to the north and south (Her-
shler et al., 1999). Our Amargosa River samples,
positioned intermediate between the Colorado
and Owens Rivers, may reflect but a single as-
pect of this complex hydrology.
Columbia River Basin.—The Columbia River
clade, although highly supported by our data,
was not a monophyletic assemblage. That is, in-
dividuals from some localities showed greater af-
finities to basins outside the present watershed.
For example, the Columbia River clade includ-
ed samples from the middle and upper Colum-
bia and lower Snake Rivers but not the upper
Snake River. The latter sample was instead sister
to the Bear River of the Northern Bonneville,
and these were sister to other northern Bon-
neville localities. The basal position of Colum-
bia
1
Klamath/Pit, and the close affinity of
Clearwater River (CLR) with Southern Bonne-
ville (SEV4, BSC2), suggested that the develop-
ing premodern Snake River exerted an early in-
fluence upon the Columbia River. The current
separation of the upper Snake and Columbia
faunas is attributable to the long intervals of iso-
lation, as well as to the extinction of Columbia
River forms caused by vulcanism on the Snake
River Plain (McPhail and Lindsey, 1986; Malde,
1991). A close relationship between the Upper
Snake and the Northern Bonneville is not sur-
prising, given a scenario of repeated exchanges
between the two, including a spectacular over-
topping of Lake Bonneville in late Pleistocene
(Gilbert, 1890). The hypothesis that upper
Snake River populations resulted from Bonne-
ville Basin immigrants (Miller and Miller, 1948)
was supported in our study by the presence of
a common haplotype in both upper Snake and
Bear Rivers (Oakey, 2001). However, the Upper
Snake reflects low haplotype diversity, which is
likely a result of local bottlenecks, extinctions,
and rapid loss of mtDNA lineages, perhaps as-
sociated with regional vulcanism or glacial pe-
riods (Smith, 1966; Malde, 1991).
One lower Columbia River locality (i.e., Des-
chutes River; DSC) did not cluster with upper
basin haplotypes but was instead sister to the
Northern Bonneville. This can, in part, be ex-
plained by the complex history of the premod-
ern Snake River and the Oregon Lakes region.
During Pliocene, a suggested outlet for the pre-
modern Snake River was through Harney and
Malheur Lakes, as the Snake passed from south-
ern Idaho to the Pacific Ocean (Smith, 1975;
Taylor, 1985:fig. 5). A subsequent connection
between the Deschutes River and the Oregon
Lakes district was of brief duration and was out-
lined by Behnke (1979) and Taylor (1985). Ap-
parently, the upper Deschutes River flowed into
the Oregon Lakes when the western flow of the
Snake River was reversed as a result of uplift.
216 COPEIA, 2004, NO. 2
Klamath-Pit clade.—The Klamath
1
Pit clade is
composed not only of samples from widely scat-
tered localities in the Klamath and Pit Rivers
but also those from south-coastal (i.e., San Ben-
ito River) and eastern California (i.e., Eagle
Lake). Two general scenarios may explain the
close relationship between the Pit River and the
south-coastal San Bonito River (Pajaro Basin).
Rhinichthys osculus may have entered the Pajaro
Basin by way of a headwater transfer with the
San Joaquin River (Snyder, 1905; Murphy,
1941). Prior to 1.5 mya, the Sacramento River
also flowed through the San Francisco Trough
to Monterey Bay, whereas the San Benito River
flowed north into San Francisco Bay (Taylor,
1985:312, fig. 38). The general extension of the
Sacramento River ichthyofauna into south-
coastal drainages was clearly demonstrated by
these patterns (Snyder, 1905), as represented an
extension of the R. osculus form in the Snake
River ( Jordan and Evermann, 1896; Cornelius,
1969).
The Pit River is centrally positioned in this
region and was the center of intense orogeny
and volcanism during Pliocene and Pleistocene.
The Klamath-Cascade region acted as a single,
coherent block when its western end was dis-
placed 340 km to the south about 20 mya (Ma-
gill and Cox, 1981). Thus, a close relationship
between Klamath and Pit Rivers may in part be
the result of these drainage realignments
(Minckley et al., 1986). Fossils from the early
Pliocene connected both Pit and Klamath Ba-
sins with the premodern Snake River as the lat-
ter drained to the Pacific Ocean (Miller and
Smith, 1967; Smith, 1975; Taylor, 1985). The po-
sition of this clade in Figure 2 points to its an-
cient connections, but the timing is clearly un-
certain, in part because of a lack of physical ev-
idence coupled with the uncertainty in aging
fossil materials (Smith et al., 2000).
Bonneville Basin and the origin of Rhinichthys os-
culus.—The numerous examples of differenti-
ated fauna in the Bonneville Basin were recog-
nized by Cope and Yarrow (1875) as stemming
from long intervals of piecemeal isolation.
Their conclusions are strongly supported by the
patterns we uncovered in R. osculus. For exam-
ple, a majority of haplotypes from the Northern
Bonneville clustered with the Deschutes River
(DSC), whereas one (i.e., Box Elder County,
UT; BOX1) was consistently sister to the Colo-
rado River. Southern Bonneville haplotypes
were also sister to the Upper Colorado, whereas
two highly divergent haplotypes were sister to
the Lower Snake (Clearwater River; CLR). Tay-
lor (1983; 1985:296, fig. 25) suggested a Late-
Miocene drainage connection between south-
eastern Idaho and the lower Colorado River Ba-
sin, a route supported by living and fossil mol-
luscs in western Bonneville Basin. Hubbs and
Miller (1948) identified this drainage as a struc-
tural trough leading to Pluvial White and Car-
penter Lakes. This north-south connection be-
tween the Bonneville Basin and the Colorado
River is also reflected in the distribution of Gila
(now Snyderichthys) copei ( Johnson and Jordan,
2000). Haplotypes of this species are separated
into northern (e.g., Bear and upper Snake Riv-
ers) and southern (e.g., Utah Lake and Sevier
River) clades, with the northern clade more ge-
netically similar to the outgroup taxon (Lepido-
meda mollispinis mollispinis) from Virgin River.
The fragmented history of the Bonneville Basin
is clearly evident, and these studies provide
compelling evidence of its role as a north-south
conduit between southern Idaho and the Col-
orado River.
Taylor’s (1985) western Bonneville route
crossed the drainage of Big Spring Creek, at the
upper end of Snake Valley (Tooele County,
UT), where Smith (1978) noted a distinct, un-
described dace that shared many ‘‘spring iso-
late’’ characters with the extinct R. deaconi (Mill-
er, 1984:table 2). Our two divergent southern
Bonneville haplotypes (i.e., Big Springs Creek
[BSC2] and Sevier River [SEV4]) differed from
conspecifics by greater than eight restriction
sites. Finding two highly divergent haplotypes at
the same locality represents an uncommon
Type-II phylogeographic situation (Avise et al.,
1987), generally attributed to secondary contact
among allopatric populations. Our study sug-
gests these divergent, southern Bonneville hap-
lotypes may represent a widespread and unde-
scribed form related to R. osculus but with an
earlier connection to the north. This is sup-
ported by the position of these Southern Bon-
neville haplotypes in our trees, and by the basal
location of Northern Bonneville, Los Angeles
and Middle Colorado Basins within their re-
spective clades. The close affinity of Colorado
River R. osculus with those in the Los Angeles
Basin, but not with Death Valley, suggests two
different invasions in that region. The Northern
Bonneville-to-Colorado-to-Los Angeles connec-
tion was likely earlier than the Lahontan-to-
Owens connection.
It is tempting to infer from these data the
origin of R. osculus in Western North America.
Patterns of haplotype distribution suggest that
the premodern Snake River and Lake Idaho
had major roles in the distribution and subse-
quent evolution of R. osculus in surrounding ba-
sins. The basal position of those basins allied to
217OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
the early Snake River (e.g., Upper Snake,
Northern Bonneville, Klamath-Pit, and Colum-
bia) could represent the earliest appearance of
modern R. osculus in the west. Bonneville hap-
lotypes join the tree at separate yet earlier po-
sitions, and may represent an early R. osculus
form in the western paleodrainages of the Mo-
have and Sonoran desert provinces (sensu
Minckley et al., 1986). The long isolation of the
Los Angeles Basin, and its sister relationships
with the Northern Bonneville and Colorado
clades suggest the possibility of an earlier R. os-
culus-like form in this region. The presence of
undescribed Rhinichthys (Peden and Hughes,
1988) in the Columbia River Basin also indi-
cates that evolution of the group may have been
northerly, possibly associated with retreating ice
(McPhail and Lindsey, 1986; Bodaly et al.,
1992). However, the early Bonneville-to-Colora-
do distribution, coupled with the accompanying
fishhook drainage, suggest that R. osculus may,
in fact, have originated much earlier, possibly
associated with Tertiary Lake Idaho.
A
CKNOWLEDGMENTS
DDO received enormous assistance collecting
fish samples from around the West (a full list of
collectors is provided in Oakey, 2001:appendix
5). However, two friends stand foremost in this
endeavor: J. Dunham and M. Andersen. Col-
lecting permits were provided by the states of
AZ, CA, ID, MT, NV, and UT, whereas the Ari-
zona State University IACUC (Institutional An-
imal Care and Use Committee) approved col-
lecting protocols. Numerous friends assisted be-
tween campus and field: J. Bann, B. Bartram, R.
Broughton, P. Brunner, J. Chesser, B. DeMarais,
E. Goldstein, A. Dauberman, D. McElroy, G.
Naylor, S. Norris, R. Olson, C. Secor, A. Tibbets,
R. Timmons, B. Trapido-Lurie, P. Unmack, T.
Velasco, and M. Wurzburger. This manuscript
represents part of a dissertation submitted by
DDO in partial requirement for the Ph.D. de-
gree at Arizona State University. Support from
a National Science Foundation Dissertation Im-
provement Grant is greatly acknowledged. This
manuscript is dedicated to the memory of Pro-
fessor W. L. Minckley of Arizona State Univer-
sity, who for 35 years studied the origin and evo-
lution of native fishes in western North Ameri-
ca. He (and colleagues) struggled mightily to
conserve this fauna against rampant water di-
version and the unbridled urban sprawl that
now characterize the ‘‘New West.’’ He was a mo-
tivating force for this study, and his death on 22
June 2001 left an inestimable void in both our
knowledge of indigenous, western North Amer-
ican fishes and the landscape within which they
evolved.
L
ITERATURE
C
ITED
A
LLARD
,M.W.,
AND
J. M. C
ARPENTER
. 1996. On
weighting and congruence. Cladistics 12:183–198.
A
LLENDORF
,F.W.,
AND
R. F. L
EARY
. 1988. Conservation
and distribution of genetic variation in a polytypic
species, the Cutthroat Trout. Conserv. Biol. 2:170–
183.
A
NDERSON
, F. E. 2000. Phylogenetic relationships
among loliginid squids (Cephalopoda: Myopsidae)
based upon analysis of multiple data sets. Zool. J.
Linn. Soc. 130:603–633.
A
RCHIE
, J. W. 1996. Measures of homoplasy, p. 153–
188. In: Homoplasy: the recurrence of similarity in
evolution. M. J. Sanderson and L. Hufford (eds.).
Academic Press, New York.
A
VISE
, J. C., A
RNOLD
, J., B
ALL
, R. M., B
ERMINGHAM
, E.,
L
AMB
, T., N
EIGEL
, J. E., R
EEB
, C. A.,
AND
N. C. S
AUN
-
DERS
. 1987. Intraspecific phylogeography: the mi-
tochondrial DNA bridge between population ge-
netics and systematics. Annu. Rev. Ecol. Syst. 18:
489–522.
B
EHNKE
, R. J. 1979. Monograph of the native trouts
of the genus Salmo of western North America. U.S.
Fish and Wildlife Service, Denver, CO.
———. 1992. Native trout of western North America.
Am. Fish. Soc., Spec. Monogr. 6:1–275.
B
ISHOP
, P. 1995. Drainage rearrangement by river cap-
ture, beheading and diversion. Prog. Phys. Geogr.
19:449–473.
B
ODALY
, R. A., J. W. C
LAYTON
,C.C.L
INDSEY
,
AND
J.
V
UORINEN
. 1992. Evolution of Lake Whitefish (Cor-
egonus clupeaformis) in North America during the
Pleistocene: genetic differentiation between sym-
patric populations. Can. J. Fish. Aquat. Sci. 49:769–
779.
C
OBURN
, M. M.,
AND
T. M. C
AVENDER
. 1992. Interre-
lationships of North American cyprinid fishes, p.
328–373. In: Systematics, historical ecology, and
North American freshwater fishes. R. L. Mayden
(ed.). Stanford Univ. Press, Stanford, CA.
C
OPE
, E. D.,
AND
H. C. Y
ARROW
. 1875. Report upon
the collections of fishes made in portions of Neva-
da, Utah, California, Colorado, New Mexico, and
Arizona, during 1871, 1872, 1873, and 1874, p.
635–703. In: United States Army engineer depart-
ment report on the geography and geology of the
explorations and surveys west of the 100th Meridi-
an, in Charge of George M. Wheeler. Vol. 5 (Zool-
ogy). Government Printing Office, Washington,
DC.
C
ORNELIUS
, R. H. 1969. The systematics and zooge-
ography of Rhinichthys osculus (Girard) in southern
California. Unpubl. master’s thesis, California State
Univ., Fullerton.
D
AWSON
, A. G. 1992. Ice Age Earth. Routledge Press,
London.
D
ELLENBAUGH
, R. H. 1873. A canyon voyage. Academ-
ic Press, New York.
D
E
M
ARAIS
, B. D., T. E. D
OWLING
,M.E.D
OUGLAS
,W.
218 COPEIA, 2004, NO. 2
L. M
INCKLEY
,
AND
P. C. M
ARSH
. 1992. Origin of Gila
seminuda (Teleostei: Cyprinidae) through introgres-
sive hybridization: implications for evolution and
conservation. Proc. Natl. Acad. Sci. USA 89:2747–
2751.
D
OUGLAS
, M. E. 1993. An analysis of sexual dimor-
phism in an endangered cyprinid fish (Gila cypha
Miller) using video image technology. Copeia 1993:
334–343.
———, W. L. M
INCKLEY
,
AND
B. D. D
E
M
ARAIS
. 1999.
Did vicariance mold phenotypes of western North
American fishes? Evidence from Gila River cypri-
nids. Evolution 53:238–246.
D
OWLING
,T.E.,
AND
B. D. D
E
M
ARAIS
. 1993. Evolution-
ary significance of introgressive hybridization in
cyprinid fishes. Nature 362:444–446.
———, C. M
ORITZ
,J.D.P
ALMER
,
AND
L. H. R
IESBERG
.
1996. Nucleic acids III: analysis of fragments and
restriction sites, p. 249–320. In: Molecular system-
atics. 2d ed. D. M. Hillis, C. Moritz, and B. K. Mable
(eds.). Sinauer Associates, New York.
D
UVERNELL
, D. D.,
AND
B. J. T
URNER
. 1998. Evolution-
ary genetics of Death Valley pupfish populations:
mitochondrial DNA sequence variation and popu-
lation structure. Mol. Ecol. 7:279–288.
F
ARRIS
, J. S. 1969. A successive approximations ap-
proach to character weighting. Syst. Zool. 18:374–
385.
F
U
, J. 2000. Toward the phylogeny of the family Lac-
ertidae—why 4,708 base pairs of mtDNA sequences
cannot draw the picture. Biol. J. Linn. Soc. 71:203–
217.
G
ILBERT
, G. K. 1890. Lake Bonneville. U.S. Geol. Surv.
Monogr. 1:1–438.
G
OLOBOFF
, P. A. 1995. Parsimony and weighting: a re-
ply to Turner and Zandee. Cladistics 11:91–104.
———. 1999. Analyzing large data sets in reasonable
times: solutions for composite optima. Ibid. 15:415–
428.
H
ANSEN
, M. M., K.-L. D. M
ENSBERG
,
AND
S. B
ERG
. 1999.
Postglacial recolonization patterns and genetic re-
lationships among whitefish (Coregonus sp.) popu-
lations in Denmark, inferred from mitochondrial
DNA and microsatellite characters. Mol. Ecol. 8:
239–252.
H
ERSHLER
, R., L. H
SIU
-P
ING
,
AND
M. M
ULVEY
. 1999.
Phylogenetic relationships within the aquatic snail
genus Tyronia: Implications for biogeography of the
North American southwest. Mol. Phylogenet. Evol.
13:377–391.
H
ILL
, D. P., R. A. B
AILEY
,
AND
A. S. R
YALL
. 1985. Active
tectonic and magmatic processes beneath Long Val-
ley caldera, eastern California: an overview. J. Geo-
phys. Res. 90(B13):11111–11120.
H
OWARD
, J. L. 1996. Paleocene to Holocene paleo-
deltas of ancestral Colorado River offset by the San
Andreas fault system, southern California. Geology
24:783–786.
———. 2000. Provenance of quartzite clasts in the Eo-
cene-Oligocene sespe formation: paleogeographic
implications for southern California and the ances-
tral Colorado River. Bull. Geol. Sci. Am. 112:1635–
1649.
H
UBBS
,C.L.,
AND
R. R. M
ILLER
. 1948. The zoological
evidence: correlation between fish distributions
and hydrographic history in the desert basins of
western United States, p. 17–144. In: The Great Ba-
sin, with emphasis on glacial and post-glacial times.
Bulletin of the Univ. of Utah 38, Biol. Ser. 10, Salt
Lake City.
———, ———,
AND
L. C. H
UBBS
. 1974. Hydrographic
history and relict fishes of the north-central Great
Basin. Calif. Acad. Sci. Mem. 7:1–259.
H
UGHES
,G.W.,
AND
A. E. P
EDEN
. 1989. Status of the
Umatilla Dace, Rhinichthys umatilla, in Canada. Can.
Field Nat. 103:193–200.
H
UNT
, C. B. 1969. Geologic history of the Colorado
River, p. 59–130. In: The Colorado River region and
John Wesley Powell. U.S. Geological Survey Profes-
sional Papers 669. Government Printing Office,
Washington, DC.
J
OHNSON
, J. B.,
AND
S. J
ORDAN
. 2000. Phylogenetic di-
vergence in Leatherside Chub (Gila copei) inferred
from mitochondrial cytochrome b sequences. Mol.
Ecol. 9:1029–1035.
J
ORDAN
, D. S. 1891. Report of explorations in Colo-
rado and Utah during the summer of 1889, with an
account of the fishes found in each of the river
basins examined. Bull. U.S. Fish Comm. 9:1–40.
———,
AND
B. W. E
VERMANN
. 1896–1900. The fishes
of North and Middle America. Bull. U.S. Nat. Mus.
47(4 parts):i–ix,1–3313.
———, ———,
AND
H. W. C
LARK
. 1930. Checklist of
the fishes and fishlike vertebrates of North and
Middle America north of the northern boundary
of Venezuela and Columbia. Rept. U.S. Comm.
Fish. 1928:1–670.
L
A
R
IVERS
, I. 1962. Fishes and fisheries of Nevada. Ne-
vada Fish and Game Commission, Reno.
M
AGILL
, J.,
AND
A. C
OX
. 1981. Post-Oligocene tectonic
rotation of the Oregon Western Cascade Range and
the Klamath Mountains. Geology 9:127–131.
M
ALDE
, H. E. 1991. Quaternary geology and structur-
al history of the Snake River plain, Idaho and
Oregon, p. 251–281. In: Quaternary nonglacial ge-
ology: conterminous U.S. R. B. Morrison (ed.).
Geological Society of America, Boulder, CO.
M
ARTINSON
, D. G., N. G. P
ISIAS
,J.D.H
AYS
,J.I
MBRIE
,
T. C. M
OORE
J
R
.,
AND
N. J. S
HACKLETON
. 1987. Age,
dating, and orbital theory of the Ice Ages: devel-
opment of a high-resolution 0–300,000 year chron-
ostratigraphy. Quart. Res. 27:1–29.
M
C
C
USKER
, M. R., E. P
ARKINSON
,
AND
E. R. L
INDSEY
.
2000. Mitochondrial DNA variation in Rainbow
Trout (Oncorhynchus mykiss) across its native range:
testing biogeographical hypotheses and their rele-
vance to conservation. Mol. Ecol. 9:2089–2108.
M
C
P
HAIL
,J.D.,
AND
C. C. L
INDSEY
. 1986. Zoogeogra-
phy of the freshwater fishes of Cascadia (the Co-
lumbia system and rivers north to the Sikine), p.
615–638. In: The zoogeography of North American
freshwater fishes. C. H. Hocutt and E. O. Wiley
(eds.). John Wiley and Sons, New York.
M
IDDLETON
, L. T., M. L. P
ORTER
,
AND
P. G. K
IMMEL
.
1985. Depositional settings of the Chalk Hills and
Glenns Ferry formations west of Bruneau, Idaho,
p. 37–53. In: Cenozoic paleogeography of west-cen-
tral United States. R. M. Flores and S. S. Kaplan
219OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
(eds.). Rocky Mountain Section—Soc. Econ. Pa-
leont. Mineral., Denver, CO.
M
ILLER
, R. R. 1946a. Gila cypha, a remarkable new spe-
cies of fish from the Colorado River in Grand Can-
yon, Arizona. J. Wash. Acad. Sci. 36:403–415.
———. 1946b. Correlation between fish distribution
and Pleistocene hydrography in eastern California
and southwestern Nevada, with a map of the Pleis-
tocene waters. J. Geol. 54:43–53.
———. 1958. Origin and affinities of the freshwater
fish fauna of western North America, p. 187–222.
In: Zoogeography. C. L. Hubbs (ed.). American As-
sociation for the Advancement of Science, Publ. 51,
Washington, DC.
———. 1984. Rhinichthys deaconi, a new species of
dace (Pisces: Cyprinidae) from southern Nevada.
Occ. Pap. Mus. Zool. Univ. Mich. 707:1–21.
———,
AND
C. L. H
UBBS
. 1960. The spiny-rayed cyp-
rinid fishes (Plagopterini) of the Colorado River
System. Misc. Publ. Mus. Zool. Univ. Mich. 115:1–
39.
———,
AND
R. G. M
ILLER
. 1948. The contribution of
the Columbia River system to the fish fauna of Ne-
vada: five species unrecorded from the state. Cop-
eia 1948:174–187.
———,
AND
G. R. S
MITH
. 1967. New fossil fishes from
Plio-Pleistocene Lake Idaho. Occ. Pap. Mus. Zool.
Univ. Mich. 654:1–24.
———,
AND
———. 1981. Distribution and evolution
of Chasmistes (Pisces: Catostomidae) in western
North America. Ibid. 696:1–46.
M
INCKLEY
, W. L. 1973. Fishes of Arizona. Arizona
Game and Fish Department, Phoenix.
———,
AND
B. D. D
E
M
ARAIS
. 2000. Taxonomy of
chubs (Teleostei, Cyprinidae, genus Gila)inthe
American southwest with comments on conserva-
tion. Copeia 2000:251–256.
———,
AND
M. E. D
OUGLAS
. 1991. Discovery and ex-
tinction of western fishes: a blink of the eye in geo-
logic time, p. 7–17. In: Battle against extinction: na-
tive fish management in the American west. W. L.
Minckley and J. E. Deacon (eds.). Univ. of Arizona
Press, Tucson.
———, D. A. H
ENDRICKSON
,
AND
C. E. B
OND
. 1986.
Geography of western North American freshwater
fishes: description and relationships to intraconti-
nental tectonism, p. 519–614. In: The zoogeogra-
phy of North American freshwater fishes. C. H. Ho-
cutt and E. O. Wiley (eds.). John Wiley and Sons,
New York.
M
ORITZ
, C., T. E. D
OWLING
,
AND
W. M. B
ROWN
. 1987.
Evolution of animal mitochondrial DNA: relevance
for population biology and systematics. Annu Rev.
Syst. Ecol. 18:269–292.
M
OYLE
, P. B. 1976. Inland fishes of California. Univ.
of Calif. Press, Berkeley.
M
URPHY
, G. 1941. A key to the fishes of the Sacra-
mento–San Joaquin Basin. Calif. Fish Game 1941:
165–171.
N
ATIONS
, D., J. C. W
ILT
,
AND
R. H. H
ELVY
. 1985. Ce-
nozoic paleogeography of Arizona, p. 335–355. In:
Cenozoic paleogeography of west-central United
States. R. M. Flores and S. S. Kaplan (eds.). Rocky
Mountain Section—Soc. Econ. Paleont. Mineral.,
Denver, CO.
N
IXON
, K. C. 1999. The parsimony ratchet, a new
method for rapid parsimony analysis. Cladistics 15:
407–414.
———,
AND
J. M. C
ARPENTER
. 1996. On consensus,
collapsibility, and clade concordance. Ibid. 12:305–
312.
O
AKEY
, D. D. 2001. Genetic and geographic variation
in Rhinichthys osculus (Teleostei: Cyprinidae) from
western North America. Unpubl. Ph.D. diss., Ari-
zona State Univ., Tempe.
P
EDEN
,A.E.,
AND
G. W. H
UGHES
. 1981. Life-history
notes relevant to the Canadian status of the Speck-
led Dace (Rhinichthys osculus). Syesis 14:21–31.
———,
AND
———. 1988. Sympatry in four species
of Rhinichthys (Pisces), including the first docu-
mented occurrences of R. umatilla in the Canadian
drainages of the Columbia River. Can. J. Zool. 66:
1846–1856.
P
LATNICK
, N. I. 2000. A re-limitation and revision of
the Australasian ground spider family Lamponidae
(Araneae: Gnaphosoidea). Bull. Am. Mus. Nat.
Hist. 245:1–328.
S
CHNEIDER
, C. J., M. C
UNNINGHAM
,
AND
C. M
ORITZ
.
1998. Comparative phylogeography and the history
of endemic vertebrates in the wet tropic rainforests
of Australia. Mol. Ecol. 7:487–498.
S
MITH
, G. R. 1966. Distribution and evolution of the
catostomid fishes of the subgenus Pantosteus, genus
Catostomus. Misc. Pub. Mus. Zool. Univ. Mich. 129:
1–132.
———. 1975. Fishes of the Pliocene Glenns Ferry For-
mation, Southwest Idaho. Univ. Mich. Mus. Paleont.
Pap. Paleont. 14:1–68.
———. 1978. Biogeography of intermountain fishes,
p. 17–42. In: Intermountain biogeography, a sym-
posium. K. T. Harper and J. L. Reveal (eds.). Great
Basin Nat. Mem. 2, Bricham Young Univ., Provo,
UT.
———. 1981. Late Cenozoic freshwater fishes of
North America. Annu. Rev. Syst. Ecol. 12:163–193.
———. 1987. Fish speciation in a western North
American Pliocene rift lake. Palaios 2:436–445.
———, M
ORGAN
, N.,
AND
E. G
USTAFSON
. 2000. Fishes
of the Mio-Pliocene Ringold Formation, Washing-
ton: Pliocene capture of the Snake River by the Co-
lumbia River. Univ. Mich. Mus. Paleont. Pap. 32:1–
47.
———, T. E. D
OWLING
,K.W.G
OBALET
,T.L
UGASKI
,
D. K. S
HIOZAWA
,
AND
R. P. E
VANS
. 2002. Biogeog-
raphy and timing of evolutionary events among
Great Basin fishes, p. 175–234. In: Great Basin
aquatic systems history. R. Hershler, D. B. Madsen
and D. R. Currey (eds). Smiths. Contrib. Earth Sci.,
No. 33. Smithsonian Institution Press, Washington,
DC.
S
NYDER
, J. O. 1905. Notes on the fishes of the streams
flowing into San Francisco Bay, California. U.S. Fish
Comm. Rept. 1904:327–338.
S
TEARLEY
,R.F.,
AND
G. R. S
MITH
. 1993. Phylogeny of
Pacific trouts and salmon (Oncorhynchus) and gen-
era of family Salmonidae. Trans. Am. Fish. Soc. 122:
1–33.
220 COPEIA, 2004, NO. 2
S
TEGNER
, W. 1954. Beyond the hundreth meridian.
Explorations of the intermontane west by J. M. Pow-
ell. Penguin Books, New York.
S
WOFFORD
,D.L.O
LSEN
, G. J., W
ADDELL
, P. J.,
AND
D.
M. H
ILLIS
. 1996. Phylogenetic inference, p. 407–
514. In: Molecular systematics. 2d ed. D. M. Hillis,
C. Moritz, and B. K. Mable (eds.). Sinauer Associ-
ates, New York.
T
AYLOR
, D. W. 1966. Summary of North American
Blancan nonmarine mollusks. Malacologia 4:1–172.
———. 1983. Late Tertiary mollusks from the lower
Colorado River Valley. Univ. Mich. Mus. Paleont.
Contrib. 26:289–298.
———. 1985. Evolution of freshwater drainages and
molluscs in western North America, p. 265–321. In:
Late Cenozoic history of the Pacific Northwest. C.
J. Hocutt and A. B. Leviton (eds.). American Asso-
ciation for the Advancement of Science Sympo-
sium, San Francisco CA.
———,
AND
G. R. S
MITH
. 1981. Pliocene molluscs and
fishes from northeastern California and northwest-
ern Nevada. Univ. Mich. Mus. Paleont. Contrib. 25:
339–413.
T
IBBETS
,C.A.,
AND
T. E. D
OWLING
. 1996. Effects of
intrinsic and extrinsic factors on population frag-
mentation in three species of North American min-
nows (Teleostei: Cyprinidae). Evolution 50:1280–
1292.
T
URNER
, H.,
AND
R. Z
ANDEE
. 1995. The behavior of
Goloboff’s tree fitness measure, F. Cladistics 11:57–
72.
U
YENO
,T.,
AND
R. R. M
ILLER
. 1963. Summary of late
Cenozoic freshwater fish records for North Ameri-
ca. Occ. Pap. Mus. Zool. Univ. Mich. 631:1–34.
W
ILLIAMS
, J. E. 1978. Taxonomic status of Rhinichthys
osculus (Cyprinidae) in the Moapa River, Nevada.
Southwest. Nat. 23:511–518.
W
ILLS
, M. A., D. E. G. B
RIGGS
,R.A.F
ORTNEY
,M.W
IL
-
KINSON
,
AND
P. H. A. S
NEATH
. 1998. An arthropod
phylogeny based on fossil and recent taxa, p. 33–
105. In: Arthropod fossils and phylogeny. G. D.
Edgecomb (ed.). Columbia Univ. Press, New York.
W
ILSON
, C. C.,
AND
P. D. N. H
EBERT
. 1998. Phylogeog-
raphy and postglacial dispersal of lake trout (Sal-
velinus namaykush) in North America. Can. J. Aquat.
Sci. 55:1010–1024.
W
OODMAN
, D. A. 1992. Systematic relationships within
the cyprinid genus Rhinichthys, p. 374–391. In: Sys-
tematics, historical ecology, and North American
freshwater fishes. R. L. Mayden (ed.). Stanford
Univ. Press, Stanford, CA.
(DDO) D
EPARTMENT OF
B
IOLOGY AND
M
USEUM
,
A
RIZONA
S
TATE
U
NIVERSITY
,T
EMPE
,A
RIZONA
85287-1501;
AND
(MED, MRD) D
EPARTMENT
OF
F
ISHERY AND
W
ILDLIFE
B
IOLOGY
,C
OLORADO
S
TATE
U
NIVERSITY
,F
T
.C
OLLINS
,C
OLORADO
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RESENT ADDRESS
: (DDO) 323
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OUTH
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mail: (MED) michael.douglas@colostate.edu.
Submitted: 26 Nov. 2002. Accepted: 22 Jan.
2004. Section editor: R. M. Wood.
221OAKEY ET AL.—SPECKLED DACE IN THE AMERICAN WEST
A
PPENDIX
1. C
OLLECTION
A
BBREVIATIONS AND
L
OCALITIES FOR
61 Rhinichthys osculus P
OPULATIONS
U
SED IN
T
HIS
S
TUDY
(S
EE
F
IG
. 1).
OTU Locality County State Lat.–Long.
1-AMR
2-ANR
3-APC
4-BCC
5-BEN
Amargosa R.
Animas R.
Apache Cr.
Black Canyon Cr.
Benner Cr.
Nye
San Juan
Yavapai
Apache
Plumas
NV
NM
AZ
AZ
CA
36
8
52
9
N 166
8
45
9
W
36
8
44
9
N 108
8
13
9
W
34
8
53
9
N 112
8
55
9
W
35
8
44
9
N 109
8
05
9
W
40
8
20
9
N 121
8
13
9
W
6-BLU
7-BOC
8-BOX
9-BRR
10-BSC
Blue R.
Bonita Cr.
Rabbit Spr.
Bear R.
Big Springs Cr.
Greenlee
Graham
Box Elder
Rich
White Pine
AZ
AZ
UT
UT
NV
33
8
20
9
N 109
8
10
9
W
33
8
25
9
N 109
8
35
9
W
41
8
24
9
N 113
8
52
9
W
41
8
47
9
N 111
8
04
9
W
38
8
45
9
N 114
8
03
9
W
11-CBC
12-TUR
13-CHV
14-CLR
15-CON
Campbell Blue Cr.
Turkey Cr.
Chevelon Cr.
Clearwater R.
Condor Canyon
Greenlee
Cochise
Apache
Clearwater
Lincoln
AZ
AZ
AZ
ID
NV
33
8
45
9
N 109
8
07
9
W
31
8
45
9
N 109
8
05
9
W
34
8
45
9
N 110
8
40
9
W
46
8
08
9
N 115
8
47
9
W
37
8
50
9
N 114
8
22
9
W
16-DOL
17-DPB
18-DSC
Dove Cr.
Diana’s Punch Bowl
Deschutes R.
Dolores
Nye
Sherman
CO
NV
OR
37
8
45
9
N 108
8
55
9
W
39
8
02
9
N 116
8
40
9
W
45
8
37
9
N 120
8
54
9
W
19-ECC
20-FRE
21-FRN
22-GAN
23-GLN
East Clear Cr.
Frenchman’s Cr.
Francis Cr.
Gance Cr.
South Canyon Cr.
Coconino
Plumas
La Paz
Elko
Garfield
AZ
CA
AZ
NV
CO
34
8
32
9
N 111
8
10
9
W
39
8
53
9
N 120
8
16
9
W
34
8
40
9
N 113
8
25
9
W
41
8
15
9
N 115
8
48
9
W
39
8
33
9
N 107
8
25
9
W
24-GRJ
25-HAR
26-HIT
27-LCH
28-LAC
Colarado R.
Marble Cr.
Coulee Cr.
Last Chance Cr.
LaVerkin Cr.
Mesa
Mono
Stevens
Plumas
Washington
CO
CA
WA
CA
UT
39
8
03
9
N 108
8
31
9
W
37
8
46
9
N 118
8
25
9
W
47
8
44
9
N 117
8
43
9
W
40
8
25
9
N 120
8
22
9
W
37
8
16
9
N 113
8
15
9
W
29-LIT
30-LVA
31-MAY
32-MOA
33-NFH
Virgin R.
Honey Lk.
Pahranagat R.
Moapa R.
Little Humboldt R.
Washington
Lassen
Lincoln
Clark
Humboldt
UT
CA
NV
NV
NV
36
8
53
9
N 113
8
55
9
W
39
8
44
9
N 120
8
02
9
W
37
8
12
9
N 115
8
02
9
W
36
8
40
9
N 114
8
40
9
W
41
8
46
9
N 117
8
20
9
W
34-NUC
35-ORB
36-PAR
Nutrioso Cr.
Owens R.
Paria R.
Greenlee
Inyo
Coconino
AZ
CA
AZ
34
8
04
9
N 109
8
13
9
W
37
8
20
9
N 118
8
30
9
W
36
8
53
9
N 111
8
36
9
W
37-PIN
38-PIT
39-RES
40-RFC
41-SAN
Eagle Lk.
Pit R.
Reese R.
Redfield Canyon
Santa Ana R.
Lassen
Lake
Nye
Graham
San Bernardino
CA
OR
NV
AZ
CA
40
8
37
9
N 120
8
59
9
W
42
8
17
9
N 120
8
23
9
W
40
8
27
9
N 117
8
03
9
W
32
8
30
9
N 110
8
20
9
W
34
8
10
9
N 117
8
10
9
W
42-SBR
43-SEV
44-SFK
45-SFR
46-SGR
San Benito R.
Sevier R.
So. Fk. Humboldt R
San Francisco R.
San Gabriel R.
San Benito
Sanpete
Elko
Greenlee
San Bernardino
CA
UT
NV
NM
CA
36
8
30
9
N 121
8
10
9
W
39
8
24
9
N 112
8
03
9
W
40
8
38
9
N 115
8
44
9
W
33
8
23
9
N 108
8
54
9
W
34
8
21
9
N 117
8
51
9
W
47-SMO
48-SOC
49-SQQ
50-TCN
51-TCT
Smoke Cr.
Sonoita Cr.
Squaw Queen Cr.
Tucannon R.
Touchet R.
Washoe
Santa Cruz
Lassen
Columbia
Walla Walla
NV
AZ
CA
WA
WA
40
8
35
9
N 119
8
58
9
W
31
8
32
9
N 110
8
46
9
W
40
8
02
9
N 120
8
30
9
W
46
8
30
9
N 118
8
02
9
W
46
8
03
9
N 118
8
41
9
W
52-TET
53-THS
54-VEL
55-WCC
Teton R.
Thousand Spr. Cr.
White R.
West Clear Cr.
Teton
Elko
Lincoln
Yavapai
ID
NV
NV
AZ
43
8
33
9
N 111
8
02
9
W
41
8
29
9
N 114
8
14
9
W
37
8
29
9
N 115
8
10
9
W
34
8
32
9
N 111
8
30
9
W
56-WHI
57-WHS
58-WYO
59-YAK
60-YMP
61-YRC
White R.
Whitmore Hot Sps.
Gros Ventre R.
Yakima R.
Yampa R.
Yreka Cr.
Rio Blanco
Mono
Sublette
Kittitas
Moffat
Siskiyou
CO
CA
WY
WA
CO
CA
40
8
00
9
N 107
8
38
9
W
37
8
36
9
N 118
8
46
9
W
44
8
10
9
N 110
8
44
9
W
46
8
57
9
N 120
8
45
9
W
40
8
31
9
N 108
8
59
9
W
41
8
40
9
N 122
8
33
9
W
